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(-) Description

Title :  CRYSTAL STRUCTURE OF UNCHARACTERIZED CONSERVED PROTEIN FROM PYROCOCCUS HORIKOSHII
 
Authors :  M. Kanagawa, Y. Minami, N. Watanabe, S. Yokoyama, S. Kuramitsu, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  06 May 07  (Deposition) - 06 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.63
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Sheet/Helix/Sheet/Sheet/Helix, Structural Genomics, Unknown Function, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kanagawa, Y. Minami, N. Watanabe, S. Yokoyama, S. Kuramitsu
Crystal Structure Of Uncharacterized Conserved Protein From Pyrococcus Horikoshii
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN PH1780
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES IN DATABASE 5-285
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SAM2Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:158 , ILE A:172 , ASP A:174 , THR A:176 , ASP A:177 , ARG A:180 , THR A:228 , ASP A:230 , VAL A:231 , ILE A:232 , TYR A:250 , SER A:251 , ILE A:252 , GLU A:253 , GLN A:254 , PRO A:256 , HOH A:6083 , HOH A:6086 , HOH A:6094 , HOH A:6102 , HOH A:6103 , HOH A:6273 , HOH A:6295BINDING SITE FOR RESIDUE SAM A 6075

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YZQ)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:16 -Pro A:17

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YZQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YZQ)

(-) Exons   (0, 0)

(no "Exon" information available for 2YZQ)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:224
 aligned with O59416_PYRHO | O59416 from UniProtKB/TrEMBL  Length:285

    Alignment length:278
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273        
         O59416_PYRHO     4 VRVKTIMTQNPVTITLPATRNYALELFKKYKVRSFPVVNKEGKLVGIISVKRILVNPDEEQLAMLVKRDVPVVKENDTLKKAAKLMLEYDYRRVVVVDSKGKPVGILTVGDIIRRYFAKSEKYKGVEIEPYYQRYVSIVWEGTPLKAALKALLLSNSMALPVVDSEGNLVGIVDETDLLRDSEIVRIMKSTELAASSEEEWILESHPTLLFEKFELQLPNKPVAEIMTRDVIVATPHMTVHEVALKMAKYSIEQLPVIRGEGDLIGLIRDFDLLKVLV 281
               SCOP domains d2yzqa2 A:1-122 Unc            haracterized protein P          H1780                                                      d2yzqa1 A:123-278 Uncharacterized protein PH1780                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CBS-2yzqA01 A:223-278                                    Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CBS-2yzqA02 A:223-278                                    Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CBS-2yzqA03 A:223-278                                    Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CBS-2yzqA04 A:223-278                                    Pfam domains (4)
         Sec.struct. author .hhhhhhee....ee....------------..eeeee.....eeeeee....----------........eee...hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhh....hhhhhh............ee...hhhhhhhhhhh....eeeee.....eeeeee.hhhhhhhhhh.--------------------------------...hhhhh............hhhhhhhhhhhhh..eeeeee...eeeeeeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yzq A   1 MRVKTIMTQNPVTITLPAT------------VRSFPVVNKEGKLVGIISVKRI----------MLVKRDVPVVKENDTLKKAAKLMLEYDYRRVVVVDSKGKPVGILTVGDIIRRYFAKSEKYKGVEIEPYYQRYVSIVWEGTPLKAALKALLLSNSMALPVVDSEGNLVGIVDETDLLRDSEIVR--------------------------------PNKPVAEIMTRDVIVATPHMTVHEVALKMAKYSIEQLPVIRGEGDLIGLIRDFDLLKVLV 278
                                    10        |-         - |      40        50  |      -   |    70        80        90       100       110       120       130       140       150       160       170       180     |   -         -         -       220       230       240       250       260       270        
                                             19           32                   53         64                                                                                                                       186                              219
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YZQ)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: CBS] (51)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (O59416_PYRHO | O59416)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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